JEPEG Functional SNP Annotation, version 1.0

The SNP-to-gene functional annotation that jepeg and jepegmix read through their annotation_file argument. Each row ties one variant to one gene under one functional category and carries the weight that category's test applies to it.

Usage

data(JEPEG_SNP_Annotation.v1.0)

Format

A data.frame with 509,570 rows and 8 columns:

rsid

dbSNP rs identifier, or . where none is recorded.

chr

Chromosome, 1-22, X or Y.

bp

Base pair position.

a1

Reference allele.

a2

Alternative allele.

geneid

Gene symbol.

categ

Functional category: PROTEIN (260,518 rows), TRANS_EQTL (94,925), CIS_EQTL (75,118), TFBS (58,695), WTH_TARGET (19,660, within a microRNA target site) or WTH_HAIR (654, within a microRNA hairpin).

wgt

Signed weight for this variant in this category.

Details

A variant appears once per (gene, category) pair it belongs to, so the 509,570 rows cover 393,303 distinct variants over 21,458 genes. 1,651 rows carry . in place of an rsid; those variants are matched on position and alleles instead.

The weight's scale and sign are category-specific — the JEPEG method uses a different proxy measure for each, a deleteriousness score for protein function and a free-energy change for microRNA binding, among others — so weights are comparable within a category and not across categories. ReadAnnotation recognises exactly the six category names below and skips any row with another, reporting the count.

References

Lee D, Williamson VS, Bigdeli TB, Riley BP, Webb BT, Fanous AH, Kendler KS, Vladimirov VI, Bacanu SA (2015). JEPEG: a summary statistics based tool for gene-level joint testing of functional variants. Bioinformatics 31(8):1176-1182. doi:10.1093/bioinformatics/btu816

Examples

if (FALSE) { # \dontrun{
data(JEPEG_SNP_Annotation.v1.0)
str(JEPEG_SNP_Annotation.v1.0)
} # }